Prof Wolfgang Wagner says research was not properly peer-reviewed and wrongly accepted by Remote Sensing

A satellite image of clouds over Earth. The paper purported to show how the Earth’s atmosphere is more efficient at releasing energy into space than is programmed into the computer models used to forecast climate change. Photograph: Ho/Reuters Ho/REUTERS

Wagner, who is the head of the Institute of Photogrammetry and Remote Sensing at the Vienna University of Technology, added he "would also like to personally protest against how the authors and like-minded climate sceptics have much exaggerated the paper's conclusions in public statements".

The paper in question – which, Wagner says, was downloaded 56,000 times within one month after its publication in July, as a result of the attention it attracted - purported to show how the Earth's atmosphere is more efficient at releasing energy into space than is programmed into the computer models used to forecast climate change.

"Satellites show energy being lost while climate models show energy still being gained," Spencer said at the time of publication. The University of Alabama, where Spencer works as a principal research scientist at the Earth System Science Center, added in a press release in July: "The natural ebb and flow of clouds, solar radiation, heat rising from the oceans and a myriad of other factors added to the different time lags in which they impact the atmosphere might make it impossible to isolate or accurately identify which piece of Earth's changing climate is feedback from man-made greenhouse gases."

But Wagner says he now accepts the subsequent criticism from other climate scientists that the peer-review process used to test the paper's findings was flawed. "As the case presents itself now, the [peer review] editorial team unintentionally selected three reviewers who probably share some climate sceptic notions of the authors … The problem is that comparable studies published by other authors have already been refuted in open discussions and to some extend also in the literature, a fact which was ignored by Spencer and Braswell in their paper and, unfortunately, not picked up by the reviewers. In other words, the problem I see with the paper by Spencer and Braswell is not that it declared a minority view (which was later unfortunately much exaggerated by the public media) but that it essentially ignored the scientific arguments of its opponents. This latter point was missed in the review process, explaining why I perceive this paper to be fundamentally flawed and therefore wrongly accepted by the journal."

Spencer is no stranger to academic controversies. He has long maintained that satellite observations showed that atmospheric temperatures were cooling rather than warming until it was shown that the satellites in question suffered from "orbital drift".

John Abraham, an associate professor at the University of St Thomas's school of engineering in Minnesota who criticised the Spencer paper upon its publication, told the Guardian: "It is remarkable that an editor-in-chief has stepped down from his role at a journal because of the publication of a flawed paper. This significant event reflects on the significance of the flaws in the paper and its review process. It is commendable that Wagner has reacted responsibly to the situation."

He continued: "Spencer and his colleagues have a long history of minimising the effects of human-caused climate change; they also have a long history of making serious technical errors. This latest paper is only one in a decade-long track record of errors that have forced Spencer to revise his work as the errors are brought to light. Spencer is well known in the scientific community for publishing high-profile papers that initially dispute global warming and only later are found to be faulty.

"This latest article reportedly showed that the climate is not as sensitive to increases in greenhouse gases. It also called into question the cause-and-effect relationship between clouds and climate change. Wolfgang's resignation was based on the quality of the review the paper received and the obvious technical errors which the paper contained."

Next week, Prof Andrew Dessler of the department of atmospheric sciences at Texas A&M University, is due to publish a paper in the journal Geophysical Research Letters offering a detailed peer-reviewed rebuttal of Spencer's paper.

Spencer responded to the resignation via his blog. He said: "I want to state that I firmly stand behind everything that was written in that paper … It appears the IPCC [Intergovernmental Panel on Climate Change] gatekeepers have once again put pressure on a journal for daring to publish anything that might hurt the IPCC's politically immovable position that climate change is almost entirely human-caused. I can see no other explanation for an editor resigning in such a situation."